Abstract: Reasonable scientific ecological compensation mechanisms that balance different interests are critical to a successful implementation of Major Function Oriented Zone (MFOZ) plan. Current studies on ecological compensation standard of MFOZ are relatively deficient. This study divided the four MFOZs in China into two groups and analyzed three classical ecological compensation theories. The two MFOZ groups were development and protection zones and three classical theories were ecological environment value theory, externality theory and public goods theory. On the basis of "protector to profit, beneficiary to compensate", an ecological compensation model was constructed. The model also took into account the willingness of the development zones to pay, and the ecological benefits and ecosystem services of the protection zones to contribute along with its influence scope. Ecological footprint and ecosystem service-driven gravity model were used to establish the compensation model for MFOZ. The four steps that accounted for the eco-compensation mechanism included compensation standard, compensation fund, distribution plan and implementation mode. Development zones paid ecological compensations to protection zones via financial payments by governments to realize the model objectives. The study also suggested funding from multiple sources, implementation of diverse and diverse participants. It was of urgent theoretical and practical importance to establish ecological compensation model that facilitated the realization of the objectives of MFOZ plan. It was also recommended that implementation of a sound ecological compensation model would encourage ecological protection, limit vandalism and provide scientific basis for balanced differential region development.